Spiribacter Genomes
Pink-lake-hillier-Australia.jpg|Hiller Lake in Australia. The reason for its color is not known but the lake is rimmed by salt and a variety of halophilic archaea, bacteria and algae call it home.|link=http://www.amusingplanet.com/2013/03/pink-lake-hillier-in-australia.html|linktext=Hiller Lake Halobacteria are 'salt loving' members of the Archaea domain (1). Halobacteria have the ability to live in environments with high salt concentrations that would preclude the growth of other types of bacteria and archaea. The group halobacteria is itself stratified based on the level of salt that microbes can tolerate. This ranges from moderate to extremely halophilic, corresponding to the level of saturation of the environment (3.5% for seawater to 37% for full saturation) (2). Of the halobacteria, the genera Salinivibrio ''and ''Halomonas are the most recognizable (2). Salinivibrio is an aerobic, gram negative, rod shaped microbe with one polar flagellum (3) while Halomonas in addition to being aerobic, gram negative, rod shaped and having many lateral and polar flagella, is famous for having a species isolated from the wreck of the Titanic (4,5). Both Salinivibrio ''and '' Halomonas are moderate halophiles. In direct contrast to these moderate halophiles, Nitrococcus mobilis is an obligate halophile that, as its name suggests is a nitrogen oxidising, motile, coccus (6). Bringing another layer of complexity to the obligate halophiles, is the haloalkaliphilic Alkalilimnicola ehrlichii ''which, in addition to being halophilic, is also alkaliphilic i.e. salt and alkaline (pH > 7.0) loving (7). Given the diversity of the halophiles it is no surprise that novel species are frequently found. In 2013, two such species were isolated in a metagenomic study of two Spanish salterns. Identification of Spiribacter Spanish saltern.jpg|Spanish saltern. Salt water is pumped onto 'threshing pads' or balsas. The salt is made naturally through evaporation.|link=http://www.eyeonspain.com/blogs/bestofspain.aspx|linktext=saltern In a large metagenomic study carried out using direct pyrosequencing, 16S rRNA sequences for a novel microbe were found indicating that it was distantly related to ''N. mobilis and A. ehrlichii ''(2). This data was based on samples collected from Isla Cristina, Spain. In samples taken from Santa Pola, Spain, similar sequences were found. Based on these findings, medium to isolate the novel microbe was developed. Two novel strains, M19-40 and UAH-SP71 were isolated from salterns with intermediate salinity in Isla Cristina and Santa Pola (2). They were found to be part of the novel ''Ectothiorhodospiraceae which are a family of purple sulphur microbes that have been shown to produce extracellular sulphur globules (2,8) . They also have the ability to photosynthesize (8). Based on the initial results of their 16S rRNA pyrosequencing, the genus Spiribacter was assigned with each strain representing a different species, Spiribater salinus (M19-40) and Spiribacter sp. UAH-SP71 (2). The complete genomes of both species were then sequenced. Pylogenetic Relationships To determine just where the Spiribacter genus fits within the Ectothiorhodospiraceae family, a phylogenetic tree was made for the Spiribacters and Ectothiorhodospiraceae ''that had been previously sequenced. ''Allochromatium vinosum DSM180 and Thioflavicoccus mobilis 8321, two purple sulfur marine bacteria which belong to the family Chromatiaceae, were used as negative controls (2). Their results showed that their initial placement of Spiribacter in the Ectothiorhodospiraceae was correct. Both strains were monophyletic (clade consisting of an ancestral species and all its descendants) and distantly related to the Arhodomonas aquaeolei DSM 8974, an aerobic chemoheterotroph and N. mobilis Nb-231 (2). The average nucleotide identity between the two strains was 77.3%, indicating that they are indeed different species within the same genus (2). The genomes of both strains were close to 2 Mbp, making them the smallest genomes described for any halophilic microbe. The genomes are circular with only one rRNA operon (2). In contrast to A. ehrilichii, ''the ''Spiribacter have simplified metabolic diversity having lost chemolithotrophic and carbon fixing pathways (2). spiripylogeny.jpg|Phylogenetic tree showing Spiribacter species and their relationship to other Ectothiorhodospiraceae.|link=http://www.ncbi.nlm.nih.gov/pubmed/24225341|linktext=(2) spirigenomesize.jpg|Comparison of Spiribacter genome size to those of other halophiles.|link=http://www.ncbi.nlm.nih.gov/pubmed/24225341|linktext=(2) Conclusions Further comparison of Spiribacter to the most abundant halophile found to date (Salinibacter ruber), shows that both have similar xanthorhodopsins (light driven proton pumps) (2,9). In contrast to Spiribater', 'Salinibacter is motile and in addition to xanthorhodopsins, has sensory rhodopsins and chemotaxis machinery (2). Salterns are thought to be eutrophic environments where motility is not necessarily needed. This makes the presence of halophiles with motility machinery puzzling. The authors hypothesize that Salinibacter together with many other high GC haloarchaea that are often isolated from salterns, could live attached to particles, a niche that is often overlooked but can explain the need for motility to commute between particles or get to the most nutrient rich areas (2). Which would suggest specialization depending on which area of the saltern a halophile calls home. Spiribacter for example may not need motility since it occupies a different niche within the ecosystem. Since the hypersaline environment of the saltern is thought to be nutrient rich, a microbe would not need to 'worry' about 'extra' genes as the energy needed to maintain a larger genome would be readily available. But, the Spiribacters have an extremely streamlined genome. One explanation would be that though there is no pressure to lose the extra genomic material, there is no pressure to keep that material either. The fact that Spiribacter may be an extremely ubiquitous genus (present in 10-25% of the world's salinities) alludes to the fact that even under energy rich conditions, this 'streamlined' genome has the advantage. Spiribacter represents another of the extremely diverse group of moderate halophiles like Salinivibrio ''and ''Halomonas. References 1. Wikipedia, Halobacteria http://en.wikipedia.org/wiki/Halobacteria 2. Lopez-Perez M'', et al.'' (2013) Genomes of "Spiribacter", a streamlined, successful halophilic bacterium. BMC Genomics 14(1):787. 3. Amoozegar MA, Schumann P, Hajighasemi M, Fatemi AZ, & Karbalaei-Heidari HR (2008) Salinivibrio proteolyticus sp. nov., a moderately halophilic and proteolytic species from a hypersaline lake in Iran. International journal of systematic and evolutionary microbiology 58(Pt 5):1159-1163. 4. Wikipedia, Halomonas salaria http://en.wikipedia.org/wiki/Halomonas_salaria 5. Wikipedia, Halomonas titanicae http://en.wikipedia.org/wiki/Halomonas_titanicae 6. Watson S & Waterbury J (1971) Characteristics of two marine nitrite oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus mobilis nov. gen. nov. sp. Archiv. Mikrobiol. 77(3):203-230. 7. Hoeft SE'', et al.'' (2007) Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor. International journal of systematic and evolutionary microbiology 57(3):504-512. 8. Wikipedia, Ectothiorhodospiraceae http://en.wikipedia.org/wiki/Ectothiorhodospiraceae 9. Lanyi JK & Balashov SP (2008) Xanthorhodopsin: a bacteriorhodopsin-like proton pump with a carotenoid antenna. Biochimica et biophysica acta 1777(7-8):684-688.